6UND

Pseudomonas fluorescens isocyanide hydratase thioimidate intermediate at 298 K XFEL data


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NON 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE8.829831% PEG 3350, 250 mM MgCl2, 125 mM Tris-HCl, 2 mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.1442.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.766α = 90
b = 57.424β = 112.74
c = 68.79γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX340-HS2018-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.3SLAC LCLSMFX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5520.199.90.9630.19758.4536005318.49
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5799.40.140.9055.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3non1.5520.11.3459214198699.860.16420.16330.190826.83
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.7161
f_angle_d0.7785
f_chiral_restr0.0479
f_plane_restr0.0049
f_bond_d0.0047
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3368
Nucleic Acid Atoms
Solvent Atoms269
Heterogen Atoms22

Software

Software
Software NamePurpose
Blu-Icedata collection
cctbx.xfeldata reduction
cctbx.primedata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction